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java.lang.Object net.sf.basedb.core.plugin.AbstractPlugin net.sf.basedb.core.plugin.AbstractAnalysisPlugin net.sf.basedb.plugins.JepExtraValueCalculator
public class JepExtraValueCalculator
This plugin caluclates extra values from a bioassayset using mathematical formulas entered by the user.
Nested Class Summary |
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Nested classes/interfaces inherited from interface net.sf.basedb.core.plugin.Plugin |
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Plugin.MainType |
Field Summary | |
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private static About |
about
Plugin description |
private RequestInformation |
configureJob
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private static PluginParameter<String> |
expressionParameter
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private PluginParameter<ExtraValueType> |
extraValueTypeParameter
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private static Set<GuiContext> |
guiContexts
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private static Set<Permissions> |
permissions
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private ThreadSignalHandler |
signalHandler
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Fields inherited from class net.sf.basedb.core.plugin.AbstractAnalysisPlugin |
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CHILD_DESCRIPTION, CHILD_NAME, CONTEXT_BIOASSAYS, CONTEXT_BIOASSAYSET, defaultGuiContexts, nameType, optionalNameType, SOURCE_BIOASSAYS, SOURCE_BIOASSAYSET, TRANSFORMATION_NAME |
Fields inherited from class net.sf.basedb.core.plugin.AbstractPlugin |
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annotationSection, configuration, COPY_ANNOTATIONS, job, OVERWRITE_ANNOTATIONS, sc |
Constructor Summary | |
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JepExtraValueCalculator()
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Method Summary | |
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void |
configure(GuiContext context,
Request request,
Response response)
Configure the plugin. |
About |
getAbout()
Get information about the plugin, such as name, version, authors, etc. |
private RequestInformation |
getConfigureJobParameters()
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Set<GuiContext> |
getGuiContexts()
Get a set containing all items that the plugin handles. |
Collection<Permissions> |
getPermissions()
Request use access to Experiment:s and ExtraValueType:s and read access to Job:s. |
RequestInformation |
getRequestInformation(GuiContext context,
String command)
This method will return the RequestInformation for a given command, i.e. |
SignalHandler |
getSignalHandler()
Get the signal handler that is handling signals on behalf of this object. |
String |
isInContext(GuiContext context,
Object item)
Check that the item is a bioassayset and that the logged in user has permission to use the current experiment. |
boolean |
requiresConfiguration()
Returns FALSE, since that is how the plugins used to work before this method was introduced. |
void |
run(Request request,
Response response,
ProgressReporter progress)
Run the plugin. |
boolean |
supportsConfigurations()
Returns TRUE, since that is how the plugins used to work before this method was introduced. |
Methods inherited from class net.sf.basedb.core.plugin.AbstractAnalysisPlugin |
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getChildDescriptionParameter, getChildNameParameter, getCurrentBioAssaySet, getCurrentExperiment, getMainType, getSourceBioAssays, getSourceBioAssaySet, getSourceBioAssaySetParameter, getSourceBioAssaysParameter, getTransformationName, getTransformationNameParameter, restrictSource |
Methods inherited from class net.sf.basedb.core.plugin.AbstractPlugin |
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checkInterrupted, cloneParameterWithDefaultValue, closeLogFile, createLogFile, done, getCopyAnnotationsParmeter, getCurrentConfiguration, getCurrentJob, getJobOrConfigurationValue, getOverwriteAnnotationsParameters, init, log, log, storeValue, storeValue, storeValues, validateRequestParameters |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface net.sf.basedb.core.plugin.Plugin |
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done, getMainType, init |
Field Detail |
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private static final About about
private static final Set<Permissions> permissions
private static final Set<GuiContext> guiContexts
private static final PluginParameter<String> expressionParameter
private ThreadSignalHandler signalHandler
private RequestInformation configureJob
private PluginParameter<ExtraValueType> extraValueTypeParameter
Constructor Detail |
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public JepExtraValueCalculator()
Method Detail |
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public About getAbout()
Plugin
getAbout
in interface Plugin
About
objectpublic boolean supportsConfigurations()
AbstractPlugin
supportsConfigurations
in interface Plugin
supportsConfigurations
in class AbstractPlugin
public boolean requiresConfiguration()
AbstractPlugin
requiresConfiguration
in interface Plugin
requiresConfiguration
in class AbstractPlugin
public Collection<Permissions> getPermissions()
getPermissions
in interface Plugin
getPermissions
in class AbstractPlugin
public void run(Request request, Response response, ProgressReporter progress)
Plugin
run
in interface Plugin
request
- Request object with the command and parametersresponse
- Response object in for the plugin to response
throughprogress
- A ProgressReporter
where the plugin can report
its progess, can be nullpublic Set<GuiContext> getGuiContexts()
InteractivePlugin
Item.REPORTER
.
This information is used by client applications to put the plugin
in the proper place in the user interface.
getGuiContexts
in interface InteractivePlugin
getGuiContexts
in class AbstractAnalysisPlugin
Set
containing Item
:s, or null
if the plugin is not concerned about itemspublic String isInContext(GuiContext context, Object item)
AbstractAnalysisPlugin
isInContext
in interface InteractivePlugin
isInContext
in class AbstractAnalysisPlugin
context
- Current guicontextitem
- The item to check.
public RequestInformation getRequestInformation(GuiContext context, String command) throws BaseException
InteractivePlugin
RequestInformation
for a given command, i.e.
the list of parameters and some nice help text.
getRequestInformation
in interface InteractivePlugin
context
- The current context of the client application,
it is one of the values found in set returned by InteractivePlugin.getGuiContexts()
command
- The command
RequestInformation
for the command
BaseException
- if there is an errorpublic void configure(GuiContext context, Request request, Response response)
InteractivePlugin
InteractivePlugin.getRequestInformation(GuiContext, String)
.
configure
in interface InteractivePlugin
context
- The current context of the client application,
it is one of the values found in set returned by InteractivePlugin.getGuiContexts()
request
- Request object with the command and parametersresponse
- Response object in for the plugin to response
throughpublic SignalHandler getSignalHandler()
SignalTarget
getSignalHandler
in interface SignalTarget
private RequestInformation getConfigureJobParameters()
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2.17.2: 2011-06-17 | ||||||||
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